Morozov's pursued a peaceful foreign policy, securing a truce with the Polish-Lithuanian Commonwealth and carefully avoiding complications with the Ottoman Empire. His domestic policy aimed at relieving limiting the privileges of foreign traders and abolishing a useless and expensive court offices. On 17 January 1648 Morozov procured the marriage of the tsar with Maria Miloslavskaya, himself marrying her sister, Anna, ten days later, both daughters of Ilya Danilovich Miloslavsky.

Morozov was regarded as a corrupt self-seeking 17th-century boyar and accused of sorcery and witchcraft. In May 1648 Muscovites rose against his faction in the Salt Riot, and the young Tsar was compelled to dismiss them and exile Boris to the Kirillo-Belozersky Monastery. Four months later, Boris secretly returned to Moscow to regain some of his power.[1]

The popular discontent demonstrated by the riot was partially responsible for Alexis' 1649 issuance of a new legal code, the Sobornoye Ulozhenie.

Throughout his reign, Alexei faced rebellions across Russia. After resolving the 1648 Salt Riot Alexei faced rebellions in 1650 in the cities of Pskov and Great Novgorod. Alexei put down the Novgorod rebellion quickly, but was unable to subdue Pskov, and was forced to promise the city amnesty in return for surrender. The MetropolitanNikon distinguished himself at Great Novgorod and in 1651 became the Tsar's chief minister.[1]

By the 1660s, Alexei's wars with Poland and Sweden had put an increasing strain on the Russian economy—Alexei's government had begun minting large numbers of copper coins in 1654, in an attempt to increase government revenue, but this instead led to a devaluation of the ruble and a severe financial crisis. As a result, angry Moscow residents revolted in the 1662 Copper Riot, which was put down violently.[1]

In 1669, the Cossacks along the Don in southern Russia erupted in rebellion. The rebellion was led by Stenka Razin, a disaffected Don Cossack who had captured the Russian terminus of Astrakhan. From 1670 to 1671, Razin seized multiple towns along the Volga River. The turning point in his campaign was his failed siege of Simbirsk in October 1670. Razin was finally captured on the Don in April 1671, and was drawn and quartered in Moscow.[1]

In 1651 Safavid troops and allied forces of the Safavid territories in Dagestan attacked Russian fortifications along the Sunzha, as the Safavids were seeking to strengthen their position in the North Caucasus. Safavid troops and allies (wali (governor) of Dagestan, Khan of Derbent, accompanied the troops. In 1653 Alexis, initially thinking about sending the Zaporozhian Cossacks, eventually decided to send an embassy to Persia for a peaceful settlement of the conflict. In August 1653 courtier Prince Ivan Lobanov-Rostov and steward Ivan Komynin traveled from Astrakhan to Isfahan. Shah Abbas II agreed to settle the conflict, stating that the conflict was initiated without his consent.

In 1653 the weakness and disorder of Poland, which had just emerged from the Khmelnytsky Uprising, encouraged Alexei to attempt to annex from her rival the old Rus’ lands. On 1 October 1653 a national assembly met at Moscow to sanction the war and find the means of carrying it out, and in April 1654 the army was blessed by Nikon, who had been elected patriarch in 1652.

In the summer of 1655, the sudden invasion by Charles X of Sweden for the moment swept the Polish state out of existence, in what became known as the Deluge. The Russians, unopposed, quickly appropriated nearly everything which was not already occupied by the Swedes, and when at last the Poles offered to negotiate, the whole grand-duchy of Lithuania was the least of the demands of Alexei. Fortunately for Poland, the Tsar and the king of Sweden now quarrelled over the apportionment of the spoils, and at the end of May 1656 Alexei, encouraged by the Habsburg emperor and the other enemies of Sweden, declared war.

Great things were expected of the Swedish war, but nothing came of it. Dorpat was taken, but countless multitudes were lost in vain before Riga. In the meantime Poland had so far recovered herself as to become a much more dangerous foe than Sweden, and, as it was impossible to wage war with both simultaneously, the Tsar resolved to rid himself of the Swedes first. This he did by the Peace of Kardis (2 July 1661), whereby Russia retroceded all her conquests.

The Polish war dragged on for six years longer and was then concluded by the Truce of Andrusovo (11 February 1667) Vitebsk, nominally for thirteen years, which proved the most durable of treaties. According to the truce, Polotsk and Polish Livonia were restored to Poland, but the more important Smolensk and Kiev remained in the hands of Russia together with the whole eastern bank of the Dnieper River. This truce was the achievement of Afanasy Ordin-Nashchokin, the first Russian chancellor and diplomat in the modern sense, who after the disgrace of Nikon became the Tsar's first minister until 1670, when he was superseded by the equally able Artamon Matveyev, whose beneficent influence prevailed to the end of Alexei's reign.

In 1653, Patriarch Nikon established a series of reforms that aimed to bring the practices of the Russian Orthodox Church into line with its Greek counterpart. Most notably, the church began to mandate the use of three fingers instead of two in making the sign of the cross. This resulted in significant dissent among the church community. Nevertheless, Alexei continued to support Nikon until 1658, when Nikon abandoned his post due to a personal insult, leaving the seat of the patriarch vacant.[3]

In 1666, the tsar convened the Great Moscow Synod, which was attended by Patriarch Macarios III of Antioch and Patriarch Paisius of Alexandria, in order to address the problems caused by Nikon. The synod agreed to formally depose Nikon, and also decided to excommunicate all who opposed the reforms of the church; those opponents broke away from the official Russian Orthodox Church to form the Old Believers movement.[3]

It is the crowning merit of the Tsar Alexei that he discovered so many great men (like Fyodor Rtishchev, Ordin, Matveyev, the best of Peter's precursors) and suitably employed them. He was not a man of superior strength of character, or he would never have submitted to the dictation of Nikon. But, on the other hand, he was naturally, if timorously, progressive, or he would never have encouraged the great reforming boyar Matveyev. His last years, notwithstanding the terrible rebellion of Stenka Razin, were deservedly tranquil.

A few private letters and an instruction to his falconers is all we have of him. But it is sufficient for Sergey Platonov to proclaim him the most attractive of Russian monarchs. He acquired the moniker Tishayshy, which means "most quiet" or "most peaceful". He received this moniker through the ways he behaved- he would be kind and friendly, but the sounds created from instruments would provoke him. Certain aspects of Russian Orthodoxy, not its most purely spiritual, but its aesthetic and worldly aspects, found in him their most complete expression. The essence of Alexei's personality is a certain spiritual Epicureanism, manifested in an optimistic Christian faith, in a profound, but unfanatical, attachment to the traditions and ritual of the Church, in a desire to see everyone round him happy and at peace, and in a highly developed capacity to extract a quiet and mellow enjoyment from all things.[4]

Alexei's first marriage to Miloslavskaya was harmonious and felicitous. She bore him thirteen children (five sons and eight daughters) in twenty-one years of marriage, and died only weeks after her thirteenth childbirth. Four sons survived her, (Alexei, Fyodor, Semyon, and Ivan), but within six months of her death, two of these were dead, including Alexei, the 15-year-old heir to the throne. The couple's children were:

Alexei remarried on 1 February 1671, Nataliya Kyrillovna Naryshkina ( 1 September 1651 – 4 February 1694). She was brought up in the house of Artamon Matveyev, whose wife was the Scottish-descended Mary Hamilton. Their children were: